Javascript is as much of a bytecode for the web as Java is a bytecode for the JVM.
It is not.
Where would we be if we could only execute Java on the JVM? Clojure and Scala transpiled into Java? Can you imagine how terrible that would be?
I can, and it won't be terrible at all. Compile times might suffer a little (but that's likely to be negligible with a good Java compiler - I think Jikes is now abandoned, but back in 2002 it was pretty much instantaneous even for huge files, unlike Sun's). I don't think you'd notice it on Scala, and likely also not in other JVM languages.
I've worked with Python extensions that compile indirectly through C, and I have no experience with Nim but it seems to do that very well and very quickly.
What exactly do you believe the problem would have been if Scala or Clojure generated Java rather than JVM bytecode?
It is not. Where would we be if we could only execute Java on the JVM? Clojure and Scala transpiled into Java? Can you imagine how terrible that would be?